From 4fe0f0f287bc35729e25109d187bafea1187a277 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Thu, 16 Jan 2025 21:22:49 +0000
Subject: [PATCH] Added stage for publishing to test.pypi.org when the tag a
 version number.

---
 Jenkinsfile                                   | 25 +++++++++++++----
 .../engine/remote/databases/ncbi/__init__.py  |  0
 .../engine/remote/databases/ncbi/genbank.py   | 27 -------------------
 3 files changed, 20 insertions(+), 32 deletions(-)
 delete mode 100644 src/automlst/engine/remote/databases/ncbi/__init__.py
 delete mode 100644 src/automlst/engine/remote/databases/ncbi/genbank.py

diff --git a/Jenkinsfile b/Jenkinsfile
index 8de8402..88a9444 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -30,11 +30,26 @@ pipeline {
             }
         }
         stage("publish") {
-            environment {
-                CREDS = credentials('4d6f64be-d26d-4f95-8de3-b6a9b0beb311')
-            }
-            steps {
-                sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${CREDS_USR}/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
+            parallel {
+                stage ("git.reslate.systems") {
+                    environment {
+                        CREDS = credentials('4d6f64be-d26d-4f95-8de3-b6a9b0beb311')
+                    }
+                    steps {
+                        sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${CREDS_USR}/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
+                    }
+                }
+                stage ("test.pypi.org") {
+                    when {
+                        tag '*.*'
+                    }
+                    environment {
+                        TOKEN = credentials('test.pypi.org')
+                    }
+                    steps {
+                        sh returnStatus: true, script: 'python -m twine upload -r testpypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
+                    }
+                }
             }
         }
     }
diff --git a/src/automlst/engine/remote/databases/ncbi/__init__.py b/src/automlst/engine/remote/databases/ncbi/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/src/automlst/engine/remote/databases/ncbi/genbank.py b/src/automlst/engine/remote/databases/ncbi/genbank.py
deleted file mode 100644
index a9415ee..0000000
--- a/src/automlst/engine/remote/databases/ncbi/genbank.py
+++ /dev/null
@@ -1,27 +0,0 @@
-import asyncio
-from Bio import Entrez
-from Bio import SeqIO
-
-# TODO Change this out for a more professional approach
-Entrez.email = "yunyangdeng@outlook.com"
-
-from automlst.engine.data.genomics import AnnotatedString, StringAnnotation
-
-
-async def fetch_ncbi_genbank(genbank_id: str) -> AnnotatedString:
-    with (await asyncio.to_thread(Entrez.efetch, db="nucleotide", id=genbank_id, rettype="gb", retmode="text")) as fetch_stream:
-        record = SeqIO.read(fetch_stream, "genbank")
-        sequence_features = list()
-        for feature in record.features:
-            start = int(feature.location.start)
-            end = int(feature.location.end)
-            qualifiers = feature.qualifiers
-            for qualifier_key in qualifiers:
-                qualifiers[qualifier_key] = set(qualifiers[qualifier_key])
-            sequence_features.append(StringAnnotation(
-                type=feature.type,
-                start=start,
-                end=end+1,  # Position is exclusive
-                feature_properties=qualifiers
-            ))
-        return AnnotatedString(name=genbank_id, sequence=str(record.seq), annotations=sequence_features)
\ No newline at end of file